Locus 8737

Sequence ID 3R_DroMel_CAF1
Location 23,324,594 – 23,324,726
Length 132
Max. P 0.733435
window14034 window14035 window14036

overview

Window 4

Location 23,324,594 – 23,324,697
Length 103
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 88.88
Mean single sequence MFE -37.65
Consensus MFE -30.45
Energy contribution -30.37
Covariance contribution -0.08
Combinations/Pair 1.16
Mean z-score -2.33
Structure conservation index 0.81
SVM decision value 0.43
SVM RNA-class probability 0.733435
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23324594 103 - 27905053
UGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAUUGCCAGUUUUCGGUGGCAUAAUUUGC----GUUUUCUAAUUAAAUGCGAUUAGGGGU-A-----
(((((((.......-)))))))((((..((((((..(((((((......))))))).......))))))...((((----((((.......)))))))).....)))-)----- ( -37.30)
>DroSec_CAF1 121913 103 - 1
UGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGAUGGCAUAAUUUGC----GUUUUCUAAUUAAAUGCGAUUAGGGCG-A-----
(((((((.......-)))))))((((((........)))))).((((((((((((........))))))...((((----((((.......)))))))).)))))).-.----- ( -39.90)
>DroSim_CAF1 126266 103 - 1
UGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGGUGGCAUAAUUUGC----GUUUUCUAAUUAAAUGCGAUUAGGGCG-A-----
(((((((.......-)))))))((((((........)))))).((((((((((((.(....).))))))...((((----((((.......)))))))).)))))).-.----- ( -39.30)
>DroEre_CAF1 128210 103 - 1
UGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGCUCUAGUGCCAGUUUUCGGUGGCAUAAUUUGC----GUUUUCUAAUUAAAUGCGAUUAGGGCG-A-----
(((((((.......-)))))))((((((........)))))).((((((((((((.(....).))))))...((((----((((.......)))))))).)))))).-.----- ( -41.80)
>DroYak_CAF1 133579 103 - 1
UGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGGUGGCAUACUUUGC----GUUUUCUAAUUAAAUGCGAUUAGGGCG-A-----
(((((((.......-)))))))((((((........)))))).((((((((((((.(....).))))))...((((----((((.......)))))))).)))))).-.----- ( -39.30)
>DroAna_CAF1 118179 114 - 1
UGUGGCUAAGGUUUGGGCCACAUGCCAAAAGCCAACUUGGCGAUUUCUAGUGCCAGUUUUCGGUGGAAUAAUUUGCUCUCGUUCUGUAAUUAAAUGCGGUAAGUGAACGCUUUU
(((((((........)))))))....((((((..(((((.((.....((((..(((.....((..((....))..))......)))..))))....)).)))))....)))))) ( -28.30)
>consensus
UGCGGCCAAGACCC_GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGGUGGCAUAAUUUGC____GUUUUCUAAUUAAAUGCGAUUAGGGCG_A_____
(((((((........)))))))((((((........)))))).((((((((((((........))))))...((((....(((....))).....)))).))))))........ (-30.45 = -30.37 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 23,324,622 – 23,324,726
Length 104
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 81.06
Mean single sequence MFE -31.28
Consensus MFE -27.61
Energy contribution -27.67
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -1.31
Structure conservation index 0.88
SVM decision value 0.27
SVM RNA-class probability 0.661014
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23324622 104 + 27905053
--GCAAAUUAUGCCACCGAAAACUGGCAAUAGAACCCGCCAAGUUGGCAUUUGGCAUGCGGCC-GGGUCUUGGCCGCAAACUCAGCAUCCAGCAUUCAGCAUCCAAC-----------
--((......(((((........)))))...(((...(((((((....))))))).(((((((-(.....))))))))......((.....)).))).)).......----------- ( -32.70)
>DroSec_CAF1 121941 104 + 1
--GCAAAUUAUGCCAUCGAAAACUGGCACUAGAACCCGCCAAGUUGGCAUUUGGCAUGCGGCC-GGGUCUUGGCCGCAAACUCAGCAUCCAGCAGUCCGCAUCCAAC-----------
--((.....((((((..(..(((((((..........))).))))..)...))))))((((((-(.....))))))).......)).....((.....)).......----------- ( -32.50)
>DroSim_CAF1 126294 112 + 1
--GCAAAUUAUGCCACCGAAAACUGGCACUAGAACCCGCCAAGUUGGCAUUUGGCAUGCGGCC-GGGUCUUGGCCGCAAACUCAGCAUCCAGCAGUCCGCAUCCAACAUCCAGCU---
--((......(((((........)))))..............(((((.((.((((.(((((((-(.....))))))))......((.....)).).))).))))))).....)).--- ( -33.20)
>DroEre_CAF1 128238 115 + 1
--GCAAAUUAUGCCACCGAAAACUGGCACUAGAGCCCGCCAAGUUGGCAUUUGGCAUGCGGCC-GGGUCUUGGCCGCAAACUCAGCAGCCAGCAACCAGUAUCCAGCAUCCAGCAUCC
--(((.....))).........(((((.((.(((...(((((((....))))))).(((((((-(.....))))))))..)))))..))))).............((.....)).... ( -35.60)
>DroYak_CAF1 133607 108 + 1
--GCAAAGUAUGCCACCGAAAACUGGCACUAGAACCCGCCAAGUUGGCAUUUGGCAUGCGGCC-GGGUCUUGGCCGCAAACUCCGCAUCCUGCAUCCAGUAUCCAGCAUCC-------
--((.......((((........))))(((.((....(((((((....))))))).(((((((-(.....))))))))......((.....)).)).))).....))....------- ( -33.30)
>DroAna_CAF1 118215 91 + 1
GAGCAAAUUAUUCCACCGAAAACUGGCACUAGAAAUCGCCAAGUUGGCUUUUGGCAUGUGGCCCAAACCUUAGCCACAAACUUCGCAUUCU---------------------------
..((...........(((.....))).....(((...((((((......)))))).((((((..........))))))...))))).....--------------------------- ( -20.40)
>consensus
__GCAAAUUAUGCCACCGAAAACUGGCACUAGAACCCGCCAAGUUGGCAUUUGGCAUGCGGCC_GGGUCUUGGCCGCAAACUCAGCAUCCAGCAGUCAGCAUCCAAC___________
..((.....((((((..(..(((((((..........))).))))..)...))))))((((((........)))))).......))................................ (-27.61 = -27.67 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 23,324,622 – 23,324,726
Length 104
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.06
Mean single sequence MFE -39.23
Consensus MFE -28.00
Energy contribution -28.12
Covariance contribution 0.11
Combinations/Pair 1.13
Mean z-score -1.36
Structure conservation index 0.71
SVM decision value 0.16
SVM RNA-class probability 0.614099
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23324622 104 - 27905053
-----------GUUGGAUGCUGAAUGCUGGAUGCUGAGUUUGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAUUGCCAGUUUUCGGUGGCAUAAUUUGC--
-----------.......((((((.(((((.....(((..(((((((.......-))))))..(((((........))))))..))).....))))).)))))).(((.....)))-- ( -37.70)
>DroSec_CAF1 121941 104 - 1
-----------GUUGGAUGCGGACUGCUGGAUGCUGAGUUUGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGAUGGCAUAAUUUGC--
-----------.((((.((((((((((.....))..)))))))).))))(((((-(((.....)))....(((.....))))))))...((((((........)))))).......-- ( -38.70)
>DroSim_CAF1 126294 112 - 1
---AGCUGGAUGUUGGAUGCGGACUGCUGGAUGCUGAGUUUGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGGUGGCAUAAUUUGC--
---.((((((..((((.((((((((((.....))..)))))))).)))).((((-(((.....)))....(((.....)))))))))))))((((.(....).)))).........-- ( -40.90)
>DroEre_CAF1 128238 115 - 1
GGAUGCUGGAUGCUGGAUACUGGUUGCUGGCUGCUGAGUUUGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGCUCUAGUGCCAGUUUUCGGUGGCAUAAUUUGC--
....((((((.(((((.((((((.....(.((((..(((((((((((.......-))))))).((.....)).))))..)))).).))))))))))).)))))).(((.....)))-- ( -49.20)
>DroYak_CAF1 133607 108 - 1
-------GGAUGCUGGAUACUGGAUGCAGGAUGCGGAGUUUGCGGCCAAGACCC-GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGGUGGCAUACUUUGC--
-------....((((((.(((((.((((((((.(((....(((((((.......-)))))))..))....(((.....)))).))))).)))))))).)))))).(((.....)))-- ( -43.80)
>DroAna_CAF1 118215 91 - 1
---------------------------AGAAUGCGAAGUUUGUGGCUAAGGUUUGGGCCACAUGCCAAAAGCCAACUUGGCGAUUUCUAGUGCCAGUUUUCGGUGGAAUAAUUUGCUC
---------------------------.....(((((...(((((((........))))))).(((.(((((.....(((((........)))))))))).))).......))))).. ( -25.10)
>consensus
___________GUUGGAUGCUGAAUGCUGGAUGCUGAGUUUGCGGCCAAGACCC_GGCCGCAUGCCAAAUGCCAACUUGGCGGGUUCUAGUGCCAGUUUUCGGUGGCAUAAUUUGC__
............................((((.(......(((((((........))))))).(((((........)))))).))))..((((((........))))))......... (-28.00 = -28.12 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:18:32 2006